Binghamton University The Open Repository @ Binghamton (The ORB) Biological Sciences Faculty Scholarship Biological Sciences 5-2015 High-quality permanent draft genome sequence of Bradyrhizobium sp Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York Rui Tian Matthew Parker Binghamton University--SUNY Rekha Seshadri T. B.K. Reddy Victor Markowitz See next page for additional authors Follow this and additional works at: https://orb.binghamton.edu/bio_fac Part of the Biology Commons Recommended Citation Tian, Rui; Parker, Matthew; Seshadri, Rekha; Reddy, T. B.K.; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Baeshen, Mohammed; Baeshen, Nabih; Kyrpides, Nikos; and Reeve, Wayne, "High- quality permanent draft genome sequence of Bradyrhizobium sp Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York" (2015). Biological Sciences Faculty Scholarship. 10. https://orb.binghamton.edu/bio_fac/10 This Article is brought to you for free and open access by the Biological Sciences at The Open Repository @ Binghamton (The ORB). It has been accepted for inclusion in Biological Sciences Faculty Scholarship by an authorized administrator of The Open Repository @ Binghamton (The ORB). For more information, please contact [email protected]. Authors Rui Tian, Matthew Parker, Rekha Seshadri, T. B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Mohammed Baeshen, Nabih Baeshen, Nikos Kyrpides, and Wayne Reeve This article is available at The Open Repository @ Binghamton (The ORB): https://orb.binghamton.edu/bio_fac/10 Tian et al. Standards in Genomic Sciences (2015) 10:24 DOI 10.1186/s40793-015-0008-y SHORT GENOME REPORT Open Access High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York Rui Tian1, Matthew Parker2, Rekha Seshadri3, TBK Reddy3, Victor Markowitz4, Natalia Ivanova3, Amrita Pati3, Tanja Woyke3, Mohammed N Baeshen6,7, Nabih A Baeshen5,6, Nikos Kyrpides3,5 and Wayne Reeve1* Abstract Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. Keywords: Root-nodule bacteria, Nitrogen fixation, Symbiosis, Alphaproteobacteria, GEBA-RNB Introduction perennial legume, Desmodium paniculatum, that is Strain Th.b2 is a representative of a widely distributed widely distributed across eastern North America [4]. Bradyrhizobium lineage used by several common le- Based on these field surveys, the Bradyrhizobium gumes indigenous to forested habitats in eastern North lineage represented by strain Th.b2 appears to be rela- America. Strain Th.b2 was sampled in 1991 from a tively host-specific to legumes in these four genera population of the annual legume Amphicarpaea brac- (Amphicarpaea, Apios, Desmodium, Hylodesmum), be- teata in Johnson City, NY. Surveys of other A. bracteata cause widespread sampling of sympatric legumes in populations in the eastern United States based on 20 eleven other genera have not detected this group [3,5,6]. isozyme markers found that strains similar or identical However, inoculation experiments are needed to under- to Th.b2 were present in 19 of 24 sites across six states stand whether the Th.b2 lineage lacks the ability to (IL, IN, WI, MI, NY, PA [1]). Based on both isozyme nodulate these other genera, or alternatively, may simply data and rRNA sequencing, isolates that were similar or be a poor competitor for nodulation in the presence of identical to Th.b2 were also detected in nodule samples other bacterial strains that are their preferred symbionts. from two common herbaceous perennial legumes, Apios It should also be noted that the eastern North American americana and Hylodesmum glutinosum, that often symbionts of Amphicarpaea, Apios, Desmodium and occur in woodland habitats together with Amphicarpaea Hylodesmum are not phylogenetically homogeneous at bracteata [2]. A multilocus sequence analysis found housekeeping loci. Horizontal transfer of the symbiosis strains in North Carolina populations of A. bracteata island (SI) region of the Bradyrhizobium chromosome [7] that were similar or identical to Th.b2 [3], and also de- from a member of the Th.b2 clade to a distantly related tected a highly similar strain on another herbaceous Bradyrhizobum lineage has apparently enabled the recipi- ent to gain the ability to interact with some of the normal * Correspondence: [email protected] legume hosts of the Th.b2 clade [3]. 1Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia Full list of author information is available at the end of the article © 2015 Tian et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Tian et al. Standards in Genomic Sciences (2015) 10:24 Page 2 of 7 Bacteria that are closely related to Th.b2 have also corresponding gene sequence of each type strain based been found in Japan associated with an Asian species on alignment using the EzTaxon-e server [14,15]. of Amphicarpaea (A. edgeworthii) [6]. Surprisingly, Minimum Information about the Genome Sequence strain Th.b2 lacks the ability to form nodules on A. (MIGS) is provided in Table 1 and Additional file 1: edgeworthii, although Japanese strains from A. edge- Table S1. worthii are effective nitrogen-fixing symbionts for the American legume A. bracteata [8,9]. These differences Symbiotaxonomy appear to be related to variation between related East Strain Th.b2 was isolated in 1991 from a population of Asian and North American strains in the synthesis of the annual legume Amphicarpaea bracteata in Johnson rhizobitoxine [8]. City, NY. Isolates that were similar or identical to Th.b2 Here we provide an analysis of the high-quality per- were also detected in nodule samples from two common manent draft genome sequence of Bradyrhizobum sp. herbaceous perennial legumes, Apios americana and Th.b2, one of the rhizobial genomes sequenced as part Hylodesmum glutinosum, that often occur in woodland of the DOE Joint Genome Institute 2010 Genomic habitats together with Amphicarpaea bracteata [2]. Encyclopedia for Bacteria and Archaea-Root Nodule Th.b2 lacks the ability to form nodules on the Asian spe- Bacteria (GEBA-RNB) project proposal [10], whose cies Amphicarpaea. edgeworthii, which is associated with properties may provide useful insights about the evolu- a strain closely related to Th.b2 from Japan [6,8]. tion of symbiotic specificity and its relationship to SI re- gion horizontal transfer in Bradyrhizobium. Genome sequencing information Genome project history This organism was selected for sequencing on the basis Organism information of its environmental and agricultural relevance to issues Classification and features in global carbon cycling, alternative energy production, Bradyrhizobium sp. Th.b2 is a motile, non-sporulating, and biogeochemical importance, and is part of the Gen- non-encapsulated, Gram-negative strain in the order omic Encyclopedia of Bacteria and Archaea, Root Nodu- Rhizobiales of the class Alphaproteobacteria. The rod lating Bacteria (GEBA-RNB) project at the U.S. shaped form has dimensions of approximately 0.5 μmin Department of Energy, Joint Genome Institute (JGI). width and 1.5-2.0 μm in length (Figure 1 Left and Center). The genome project is deposited in the Genomes On- It is relatively slow growing, forming colonies after 6–7 Line Database [16] and a high-quality permanent draft days when grown on half strength Lupin Agar (½LA) [11], genome sequence in IMG [17]. Sequencing, finishing tryptone-yeast extract agar (TY) [12] or a modified yeast- and annotation were performed by the JGI using state of mannitol agar (YMA) [13] at 28°C. Colonies on ½LA are the art sequencing technology [18]. A summary of the opaque, slightly domed and moderately mucoid with project information is shown in Table 2. smooth margins (Figure 1 Right). Figure 2 shows the phylogenetic relationship of Growth conditions and genomic DNA preparation Bradyrhizobium sp. Th.b2 in a 16S rRNA gene sequence Bradyrhizobium sp. Th.b2 was cultured to mid logarith- based tree. This strain is phylogenetically most closely mic phase in 60 ml of TY rich media on a gyratory related to the type strains Bradyrhizobium icense LMTR shaker at 28°C [19]. DNA was isolated from the cells 13T and Bradyrhizobium paxllaeri LMTR 21T, with a using a CTAB (Cetyl trimethyl ammonium bromide) 16S rRNA gene sequence identity of 99.77% to the bacterial genomic DNA isolation method [20]. Figure 1 Images of Bradyrhizobium sp. Th.b2 using scanning (Left) and transmission (Center) electron microscopy as well as light microscopy to visualize colony morphology on solid media (Right). Tian et al. Standards in Genomic Sciences (2015) 10:24 Page 3 of 7 Figure 2 Phylogenetic tree highlighting the position of Bradyrhizobium sp. Th.b2 (shown in blue print) relative to other type and non-type strains in the Bradyrhizobium genus using a 1,310 bp intragenic sequence of the 16S rRNA gene. Azorhizobium caulinodans ORS 571T sequence was used as an outgroup. All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 5.05 [21].